[gmx-users] Problem with Na

Mauricio Arenas Salinas marenas at usach.cl
Fri Dec 5 19:07:01 CET 2003

hi All:
i try to do MD for protein with Na and water,  but when 
the EM finishes, the final structure does not 
present/display moleculas of Na. To that can have this? 
and q I can make to solve it?

Include forcefield parameters
#include "ffgmx2.itp"

; Include chain topologies
#include "cysk_A.itp"
#include "cysk_B.itp"
#include "ions.itp"

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
SOL             23792
Na                 12

Thank you very much

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